tbuckley/cabot-search huggingface dataset:
P1373: TACKLING IMMUNOLOGICAL FINDINGS AS SURROGATE MARKERS OF HISTOLOGICAL SEVERITY AND RESPONSE TO THERAPY IN ACUTE GASTROINTESTINAL GRAFT-VERSUS-HOST DISEASE
Authors: M. Sousa-Pimenta, J. Freitas, E. Couto, P. Coelho, R. Branca, C. Pinho Vaz, L. Leite, A. Campos
Journal: HemaSphere (2022)

Background: Acute digestive tract graft-versus-host disease (GI-GVHD) is a potential complication for patients receiving allogeneic hematopoietic stem cell transplants (HSCT). The disease burden and response to therapy rely on a dynamic system: the hematopoietic stem cells (HSC) receptor characteristics (baseline degree of immune dysfunction, bone marrow microenvironment, bone marrow and gut microbiomes); the HSC donor characteristics and graft relative cellular composition. Aims: To retrospectively evaluate the role of immune reconstitution kinetics and conventional inflammatory biomarkers in the burden and response to therapy of patients with acute GI-GVHD. Methods: Cases of acute GI-GVHD after allogeneic HSCT occurring between 2016 and 2021 were assessed. The ratio of CD3+/CD34+ infused cells, the neutrophil-to-lymphocyte (NLR), lymphocyte-to-monocyte (LMR) and fibrinogen to albumin (FTA) ratios at the onset of GI-GVHD were analyzed. Central tendency measures were plotted against histological and clinical MAGIC (Mount Sinai Acute GVHD International Consortium) scores related to GI-GVHD and a multivariate analysis was performed to exclude confounding factors. Only patients with engraftment and diagnosed with GI-GVHD were included. Results: Forty-seven patients were included in the analysis (males=30), 57.4% receiving HSC from unrelated donors (n=27). At the diagnosis of GI-GVHD, the NLR was 3.4±2.3 for stage II histological grading (n=14); 6.4±6.5 for stage III (n=14) and 21.6±23.6 for stage IV (n=4); whilst LMR averaged 3.4±1.8; 1.6±1.4 and 0.7±0.4, respectively. These ratios did not correlate with the MAGIC score at diagnosis; however, the ratio of infused CD3+/CD34+ cells varied from 0.51±0.31x102 (if 3 points were achieved in gastrointestinal clinical grading) to 1.65±2.23x102 (in patients scoring 4), showing a tendency yet it did not achieve statistical significance. No significant correlation with response to steroid therapy was found. Summary/Conclusion: Overall, the higher the GI-GVHD histological score at diagnosis, the higher the NLR and the lower the LMR. In our analysis, the ratio of CD3+/CD34+ infunsed cells lost significance after adjustment for provenience of HSC. The FTA ratio had no significance as a GI-GVHD severity and/or response-related biomarker. Even though general parameters of immune reconstitution kinetics allow predicting the severity of the colon mucosa damage, they do not relate with clinical severity and response to therapy. The first two authors contributed equally to this work.
P1364: HLA MISMATCHED UNRELATED STEM CELL TRANSPLANTATION USING ANTITHYMOCYTE GLOBULIN IS A SUITABLE ALTERNATIVE FOR PATIENTS LACKING HLA-MATCHED UNRELATED DONORS: SINGLE CENTER LONG-TERM FOLLOW-UP DATA ANAL
Authors: L. Wang, P. Kong, L. Zhu, Y. Feng, T. Chen, J. Liu, C. Zhang, L. Gao, S. Gao, H. Liu, L. Gao, X. Zhang
Journal: HemaSphere (2022)

Background: Antithymocyte globulin (ATG) can improve the outcome of HLA mismatched unrelated transplantation, but there is limited data to compare HLA mismatched unrelated transplantation with matched unrelated transplantation both under condition of ATG-containing regimen. Aims: To compare HLA mismatched unrelated transplantation with matched unrelated transplantation both under condition of ATG-containing regimen. Methods: A total of 186 patients with hematological malignancies who underwent a first allo-SCT from an HLA-matched (10/10) or mismatched (9/10 or 8/10) unrelated donor from Chinese bone marrow bank and Taiwan Tzu Chi bone marrow bank following ATG-containing condition was retrospectively analyzed. A total dose of 10mg/kg ATG- Genzyme or 20mg/kg ATG- Fresenius was given from days -5 to days -2. 114 patients received HLA 10/10 fully matched, while 68 received a 9/10 and 4 received an 8/10 mismatched unrelated donor allo-SCT. OS, RFS and GRFS was calculated by the Kaplan-Meier method and the differences between groups were assessed by the log-rank test, and multivariate analysis was carried out by Cox regression model. The cumulative incidence of relapse, NRM, grade II-IV aGVHD, cGVHD and extensive cGVHD was estimated by competing risk model and compared by Gray test. Multivariate analysis was conducted by Fine and Gray regression model. Results: the median follow-up time of HLA matched transplantation and mismatched transplantation were 24 months and 21 months, respectively (P = 0.333). Univariate analysis showed that there was no significant difference in OS (78.7% vs 73.9%, P = 0.766), RFS (61.9% vs 54.8%, P = 0.464) and GRFS (46.6% vs 30.7%, P = 0.105) between HLA matched and mismatched transplantation. Multivariate analysis showed that HLA mismatch did not affect OS, RFS or GRFS (P = 0.654, P = 0.811, and P = 0.114, respectively). Univariate analysis showed no significant difference in CIR (26.1% vs 32.6%, P = 0.531), NRM (12.0% vs 12.6%, P = 0.800), cumulative incidence of cGVHD (45.3% vs 27.7%, P = 0.293) and cumulative incidence of extensive cGVHD (26.7% vs 23.4%, P = 0.635) between matched and mismatched transplantation. The cumulative incidence of grade II-IV aGVHD was higher in HLA mismatched transplantation (4.4% vs 12.3%, P = 0.046). Multivariate analysis showed that HLA mismatch was not a risk factor for CIR, NRM, cGVHD and extensive cGVHD (P = 0.44, P = 0.88, P = 0.32, P = 0.9, respectively). HLA mismatched transplantation had higher risk of grade II-IV aGVHD (HR = 2.98, P = 0.047). Summary/Conclusion: Although the incidence of aGVHD in HLA mismatched unrelated hematopoietic stem cell transplantation is higher, ATG can improve the outcome of HLA mismatched transplantation, and the survival is equivalent to that of HLA matched unrelated hematopoietic stem cell transplantation.
Nutritional deficiency in an intestine-on-a-chip recapitulates injury hallmarks associated with environmental enteric dysfunction
Authors: Amir Bein, Cicely W. Fadel, Ben Swenor, Wuji Cao, Rani K. Powers, Diogo M. Camacho, Arash Naziripour, Andrew Parsons, Nina LoGrande, Sanjay Sharma, Seongmin Kim, Sasan Jalili-Firoozinezhad, Jennifer Grant, David T. Breault, Junaid Iqbal, Asad Ali, Lee A. Denson, Sean R. Moore, Rachelle Prantil-Baun, Girija Goyal, Donald E. Ingber
Journal: Nature Biomedical Engineering (2022)

Abstract Environmental enteric dysfunction (EED)—a chronic inflammatory condition of the intestine—is characterized by villus blunting, compromised intestinal barrier function and reduced nutrient absorption. Here we show that essential genotypic and phenotypic features of EED-associated intestinal injury can be reconstituted in a human intestine-on-a-chip lined by organoid-derived intestinal epithelial cells from patients with EED and cultured in nutrient-deficient medium lacking niacinamide and tryptophan. Exposure of the organ chip to such nutritional deficiencies resulted in congruent changes in six of the top ten upregulated genes that were comparable to changes seen in samples from patients with EED. Chips lined with healthy epithelium or with EED epithelium exposed to nutritional deficiencies resulted in severe villus blunting and barrier dysfunction, and in the impairment of fatty acid uptake and amino acid transport; and the chips with EED epithelium exhibited heightened secretion of inflammatory cytokines. The organ-chip model of EED‐associated intestinal injury may facilitate the analysis of the molecular, genetic and nutritional bases of the disease and the testing of candidate therapeutics for it.
P425: ROLE OF LYSOSOMAL-ASSOCIATED GENE LAPMT4B IN LEUKEMIA
Authors: J. Delgado-Martínez, J. M. Cornet-Masana, L. Cuesta-Casanovas, J. M. Carbó, L. Clément-Démange, R. M. Risueño
Journal: HemaSphere (2022)

Background: Despite the efforts to find druggable targets in acute myeloid leukemia (AML), successful therapeutic approaches are needed in this disease. Due to the particular characteristics of lysosomes in cancer, the clinical relevance of key lysosomal genes’ expression was searched in public repositories. LAPTM4B gene expression was found to be directly correlated with a worse clinical outcome in AML. Aims: To decipher the role of the lysosome-associated gene LAPTM4B in AML will be the main objective of this study. Methods: Generation of AML cells overexpressing both LAPTM4B isoforms (35kDa -long- and 24kDa -short) were obtained by lentiviral transduction. Sensitivity to chemoresistance was measured by flow cytometry. To determine the role of LAPTM4B in the leukemia regeneration capacity, conditioned NSG mice were transplanted with both LAPTM4B isoforms-expressing AML cells and the engraftment was analysed by flow cytometry. Activation of key secondary messengers was measured by luciferase response elements and Western Blot. Results: LAPTM4B overexpression directly correlated with a higher resistance to cytarabine. LAPTM4B short isoform presented an increased clonogenic potential versus the long isoform. Interestingly, a competitive bone marrow transplantation assay confirmed this effect in terms of in vivo engraftment capacity. Moreover, LAPTM4B-mediated activation was able to induce MAPK signalling in the leukemic cell context. Summary/Conclusion: LAPTM4B overexpression not only increases the regeneration potential but also confers resistance to cytarabine, suggesting an effect in the maintenance of leukemia. In summary, this study will increase the knowledge of the role of lysosomes in leukemogenesis, and additionally, it will help to identify new lysosome-related biomarkers.
Accounting for Errors in Data Improves Divergence Time Estimates in Single-cell Cancer Evolution
Authors: Kylie Chen, Jiří C Moravec, Alex Gavryushkin, David Welch, Alexei J Drummond
Journal: Molecular Biology and Evolution (2022)

Abstract Single-cell sequencing provides a new way to explore the evolutionary history of cells. Compared to traditional bulk sequencing, where a population of heterogeneous cells is pooled to form a single observation, single-cell sequencing isolates and amplifies genetic material from individual cells, thereby preserving the information about the origin of the sequences. However, single-cell data are more error-prone than bulk sequencing data due to the limited genomic material available per cell. Here, we present error and mutation models for evolutionary inference of single-cell data within a mature and extensible Bayesian framework, BEAST2. Our framework enables integration with biologically informative models such as relaxed molecular clocks and population dynamic models. Our simulations show that modeling errors increase the accuracy of relative divergence times and substitution parameters. We reconstruct the phylogenetic history of a colorectal cancer patient and a healthy patient from single-cell DNA sequencing data. We find that the estimated times of terminal splitting events are shifted forward in time compared to models which ignore errors. We observed that not accounting for errors can overestimate the phylogenetic diversity in single-cell DNA sequencing data. We estimate that 30–50% of the apparent diversity can be attributed to error. Our work enables a full Bayesian approach capable of accounting for errors in the data within the integrative Bayesian software framework BEAST2.
P378: THE PROGNOSIS FACTORS OF CAR-T THERAPY IN PATIENTS WITH RELAPSED/REFRACTORY B-ALL
Authors: Y. Wang, X. Hu, D. Zhang, Q. Gao, X. Zhai, H. Wang, Y. Gao, Y. Miao, Y. Guo, W. Zhang, X. Ru, X. Li, F. Guan
Journal: HemaSphere (2022)

Background: CAR-T therapy showed good clinical efficacy on relapsed/refractory B-ALL (R/R B-ALL) patients. However, some latest studies revealed that most patients tend to relapse during long-term follow-up after CAR-T infusion. Few studies have examined the factors associated with the prognosis of R/R B-ALL patients. Aims: The aim of the study is to investigate the factors associated with the long-term survival of R/R B-ALL patients after CAR-T therapy. Methods: Thirty-eight R/R B-ALL patients were included in the study. Patients received CAR-T cells infusion from May 2015 to August 2018 in Shaanxi Provincial People’s Hospital. Peripheral blood mononuclear cells were collected, and CD3+ cells were sorted. CAR-T cells were prepared by lentivirus. These cells were transfused 3 to 5 days after lymphocyte removal. Bone marrow smears, flow cytometry, and QT-PCR were used to assess the development of disease between 2 and 4 weeks after infusion. The endpoint of follow-up was the time of death or Feb 15, 2022. Cox regression models were used to analyse prognosis factors. Results: The median age of the 38 patients was 25 years (6-59 years), including 21 males and 17 females. 26.3% (10/38) of patients had leukemic cells higher than 30% in their bone marrow smears. There were 34.21% (13/38) of patients with Ph(+), 34.21% (13/38) with extramedullary disease (EMD), 10.52% (4/38) with MLL-AF4 fusion gene (+), and 5.26% (2/38) had received HSCT prior to CAR-T therapy. Within 4 weeks of CAR-T cells infusion, 86.84% (33/38) of patients achieved MRD (-). 13 patients were disease-free by Feb 15, 2022. For all the 38 patients, the median OS and DFS were 19 months and 16.5 months. We found that a higher proportion of leukemic cells in bone marrow, MRD (+) after CAR-T infusion and the presence of the MLL-AF4 fusion gene could predict a worse prognosis. We found that sex, Ph (+), and HSCT after CAR-T infusion is not associated with the long-term survival of patients. Patients who had received maintenance therapy after CAR-T therapy showed better OS (49 months vs 9 months, P<0.001) and DFS (49 months vs 6 months, P<0.001) compared to those who received no maintenance therapy. In addition, we unexpectedly found that patients with EMD showed better OS (49 months vs 15 months, P=0.019) and DFS (49 months vs 12 months, P=0.045) than those without EMD. Summary/Conclusion: R/R B-ALL patients could achieve long-term survival with CAR-T cell therapy. The proportion of leukemic cells in bone marrow, MRD(+), and the presence of the MLL-AF4 fusion gene could predict a worse prognosis of R/R B-ALL patients. We found that maintenance treatment after CAR-T therapy could significantly improve patients’ long-term survival and disease-free time, while HSCT showed no significant benefit to long-term prognosis.
P614: SUBCLONAL ARCHITECTURE OF CHROMOSOMES REVEALED BY SINGLE-CELL ANALYSIS OF GENE EXPRESSION IN A PATIENT WITH CLONAL EVOLUTION OF RELAPSING/REFRACTORY CLL
Authors: J. Kotaskova, T. Kurucova, K. Reblova, M. Valisova, K. Zavacka, A. Mareckova, M. Bohunova, S. Pavlova, J. Malcikova, V. Navrkalova, M. Jarosova, M. Doubek, K. Plevova, S. Pospisilova
Journal: HemaSphere (2022)

Background: Chronic lymphocytic leukemia (CLL) manifests by remarkable intraclonal heterogeneity of genomic defects, especially in patients with relapsed/refractory disease, often connected with complex karyotype. In cancer cells, chromosomal changes are often multiple and complex. Aberrations can be present only in subclones and often underlie disease refractoriness. Using the bulk analysis such as WGS, WES, or genomic array to precisely determine the co-occurrence of aberrations in the individual cell provides limited information. Aims: To perform an in-depth, single-cell RNA sequencing (scRNAseq) study of subclonal changes associated with relapsed/refractory CLL. Methods: A bulk analysis of DNA from separated malignant cells using comprehensive NGS panel LYNX (PMID 34082072) was performed on a representative CLL case at three time-points (TPs): at dg (TP1, month 0, Rai II), before first therapy (TP2, month 19) and during relapse (TP3, month 59). Simultaneously, the transcriptome was analyzed using scRNAseq (Chromium system, 10x Genomics) in 2330 cells (TP1), 2397 cells (TP2), and 1902 cells (TP3). A detailed data analysis was carried out with the Seurat R package. In addition, we used the InferCNV tool to detect the chromosomal aberrations in every tested cell. We identified multiple chromosomal changes and compared the findings with the results of bulk DNA analysis using a genomic array (ThermoFisher Scientific) and FISH. Results: We detected a number of aberrations that were already present at TP1, including del13q, del11q, mutations in NOTCH1, RPS15, ZMYM3, and minor mutations in TP53 and ATM. At TP2, additional changes comprised mutations in PIM1, XPO1, and del(3q). Between TP2 and TP3, the patient underwent several treatment lines (FCR, BR, COP) without an apparent therapeutic effect. The cells from TP3 carried complex changes, including additional mutations in BIRC3 and RB1. Unsupervised clustering of scRNAseq gene expression data defined major clones bearing aberrations (losses on chromosomes 1, 9, 13, 17, 18). Moreover, these clones were composed of cells with additional aberrations defining a number of separate subclones. The proportion of subclones was typically under the detection limit of the genomic array and showed extreme intraclonal heterogeneity of the relapsed/refractory CLL case. Summary/Conclusion: We showcase how genomic alterations influence the expression of affected genes. Such fact can be exploited to reconstruct chromosomal disruptions in individual cells using scRNAseq and to uncover the subclonal architecture of the disease. Grants: MH-CZ_AZV_NU20-08-00314, MH-CZ_AZV_NV19-03-00091, MEYS-CZ_MUNI/A/1330/2021, MH-CZ_RVO_65269705.
P852: NEOANTIGENS PREDICTED BY THE GNE NEOANTIGEN PIPELINE IN PATIENTS DIAGNOSED WITH DE NOVO MULTIPLE MYELOMA
Authors: Y. Jiang, C. Henneges, S. Ruppert, P. Kimes, A. Amitai, A. Qamra, C. Dos Santos, J. N. Paulson, A. Bazeos
Journal: HemaSphere (2022)

Background: Neoantigens are tryptic peptides expressed and presented on MHC-I characteristic for specific tumor mutations. They enable immune surveillance against cancer and may be potential targets for individualized cancer immuno-therapy. Aims: Here we present neoantigen evaluations from reprocessing de novo Multiple Myeloma patients recruited into the CoMMpass study. Methods: Whole Exome/Genome Sequencing data as well as RNA-sequencing data was provided by the Multiple Myeloma Research Foundation CoMMpass (SM) Longitudinal Study (research.themmrf.org) [NCT01454297]. Data was processed with the GNE/Roche neoantigen pipeline applying Mutect/Strelka for mutation calling, RNAseq and hlahd for HLA haplotyping prior to predicting peptide binding affinity and rank using NetMHCpan 4.0. Only strong binding peptides (rank score <0.5) are displayed here and analyzed using the nested-model approach: the baseline model of primary therapy (PI, IMiD, both) was extended by a term for presence of individual neoantigens in a gene (prevalence >=5%) for modeling Progression-free (PFS) and Overall Survival (OS) and Number of Progression Events during Observation period. Neoantigens are reported if the Likelihood-Ratio-Test was statistically significant for the Cox PH model or a Poisson regression at the 5% level, or if the AIC was better than the reference model. We also report the c-Index and calibration slope, estimated on a predefined training:validation split. Results: In N=730 patients, we identified nine proteins with high affinity neoantigens in total (LRT p-value<0.05): MT-CYB, IGHJ5, MAGEC1, IGKV1_5, MT_ND1, IGLV3_1, KRAS, AC245369.1, and NRAS. All, except NRAS (p=0.055), had a statistically significant Risk-Ratio when included in the Poisson regression model. Of these, IGHJ5 and IGKV1-5 correlated with PFS; MT-ND1 and KRAS correlated with OS. HR and Risk-Ratios with 95% CI in Table. Neoantigens occur at different frequencies ranging from 4.5% to 31.1% in the study population. The most commonly shared neoantigens are from IGLV3-1 (31.1%). Mapping neoantigens to protein domains using the PFAM database, they are present in domains related to energy turn-over (PF00032, PF00033), RAS signaling (PF00071) or in the Ig-like domain (PF07686). Image:Summary/Conclusion: We identified nine neoantigens, including two pairs each affecting PFS and OS, that had an effect on the number of progression event rate. Most were associated with immuno-globulin chain mutations, four were found as mitochondrial mutations and or being part of signaling. More data is needed to determine the correlations of these neoantigens with clinical and cytogenetic risk factors in patients with multiple myeloma. In addition, further studies are needed to determine factors that affect the commonality of neoantigens in this population.
UK must focus on diagnostics needed to cut antimicrobial resistance, says review chair
Authors: Jacqui Wise
Journal: BMJ (2022)

A major review in 2016 concluded that antimicrobial resistance, if left unchecked, could account for 10 million global deaths a year by 2050. <b>Jacqui Wise</b> reports from a parliamentary session discussing how well the UK is mitigating the risk of another pandemic
Effect of Laparoscopic Sleeve Gastrectomy vs Roux-en-Y Gastric Bypass on Weight Loss, Comorbidities, and Reflux at 10 Years in Adult Patients With Obesity
Authors: Paulina Salminen, Sofia Grönroos, Mika Helmiö, Saija Hurme, Anne Juuti, Risto Juusela, Pipsa Peromaa-Haavisto, Marja Leivonen, Pirjo Nuutila, Jari Ovaska
Journal: JAMA Surgery (2022)

<h3>Importance</h3> Long-term results from randomized clinical trials comparing laparoscopic sleeve gastrectomy (LSG) with laparoscopic Roux-en-Y-gastric bypass (LRYGB) are limited. <h3>Objective</h3> To compare long-term outcomes of weight loss and remission of obesity-related comorbidities and the prevalence of gastroesophageal reflux symptoms (GERD), endoscopic esophagitis, and Barrett esophagus (BE) after LSG and LRYGB at 10 years. <h3>Design, Setting, and Participants</h3> This 10-year observational follow-up evaluated patients in the Sleeve vs Bypass (SLEEVEPASS) multicenter equivalence randomized clinical trial comparing LSG and LRYGB in the treatment of severe obesity in which 240 patients aged 18 to 60 years with median body mass index of 44.6 were randomized to LSG (n = 121) or LRYGB (n = 119). The initial trial was conducted from April 2008 to June 2010 in Finland, with last follow-up on January 27, 2021. <h3>Interventions</h3> LSG or LRYGB. <h3>Main Outcomes and Measures</h3> The primary end point was 5-year percentage excess weight loss (%EWL). This current analysis focused on 10-year outcomes with special reference to reflux and BE. <h3>Results</h3> At 10 years, of 240 randomized patients (121 randomized to LSG and 119 to LRYGB; 167 women [69.6%]; mean [SD] age, 48.4 [9.4] years; mean [SD] baseline BMI, 45.9 [6.0]), 2 never underwent surgery and there were 10 unrelated deaths; 193 of the remaining 228 patients (85%) completed follow-up on weight loss and comorbidities, and 176 of 228 (77%) underwent gastroscopy. Median (range) %EWL was 43.5% (2.1%-109.2%) after LSG and 50.7% (1.7%-111.7%) after LRYGB. Mean estimate %EWL was not equivalent between the procedures; %EWL was 8.4 (95% CI, 3.1-13.6) higher in LRYGB. After LSG and LRYGB, there was no statistically significant difference in type 2 diabetes remission (26% and 33%, respectively;<i>P</i> = .63), dyslipidemia (19% and 35%, respectively;<i>P</i> = .23), or obstructive sleep apnea (16% and 31%, respectively;<i>P</i> = .30). Hypertension remission was superior after LRYGB (8% vs 24%;<i>P</i> = .04). Esophagitis was more prevalent after LSG (31% vs 7%;<i>P</i> &lt; .001) with no statistically significant difference in BE (4% vs 4%;<i>P</i> = .29). The overall reoperation rate was 15.7% for LSG and 18.5% for LRYGB (<i>P</i> = .57). <h3>Conclusions and Relevance</h3> At 10 years, %EWL was greater after LRYGB and the procedures were not equivalent for weight loss, but both LSG and LRYGB resulted in good and sustainable weight loss. Esophagitis was more prevalent after LSG, but the cumulative incidence of BE was markedly lower than in previous trials and similar after both procedures. <h3>Trial Registration</h3> ClinicalTrials.gov Identifier:NCT00793143